Read AMBER Coordinate files

Usage

"read.crd"(file, ...)

Arguments

file
name of crd file to read.
...
arguments passed to and from functions.

Description

Read coordinate data from an AMBER coordinate / restart file.

Details

Read a AMBER Coordinate format file.

Value

A list object of type ‘amber’ and ‘crd’ with the following components:
xyz
a numeric matrix of class ‘xyz’ containing the Cartesian coordinates.

velocities
a numeric vector containg the atom velocities.

time
numeric, length of the simulation (applies to Amber restart coordinate files).

natoms
total number of atoms in the coordinate file.

box
dimensions of the box.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. http://ambermd.org/formats.html

Note

See AMBER documentation for Coordinate format description.

Examples

## Read Amber PRMTOP and CRD files
prm <- read.prmtop(system.file("examples/crambin.prmtop", package="bio3d"))
crd <- read.crd(system.file("examples/crambin.inpcrd", package="bio3d"))

## Convert to PDB format
pdb <- as.pdb(prm, crd)




 Summary of PDB generation:
 .. number of atoms in PDB determined by 'xyz'

 ..       46 atom(s) from 'string' selection 
 ..       46 atom(s) in final combined selection 

 .. number of atoms in PDB:  639 
 .. number of calphas in PDB: 46 
 .. number of residues in PDB: 46 





## Atom selection
ca.inds <- atom.select(prm, "calpha")




 Summary of PDB generation:
 .. number of atoms in PDB determined by 'xyz'

 ..       46 atom(s) from 'string' selection 
 ..       46 atom(s) in final combined selection 

 .. number of atoms in PDB:  639 
 .. number of calphas in PDB: 46 
 .. number of residues in PDB: 46

See also

read.prmtop, read.ncdf, as.pdb, atom.select, read.pdb, read.crd.charmm

Author

Lars Skjaerven